Medline plain importer test #354

boceckts · 2015-11-17T11:50:48Z

Fixed IndexOutOfBounds for MedlinePlainImporter when Testfile has lines with too few characters. Removed unreachable code. Created 100% Testcoverage for MedlinePlainImporter.

simonharrer · 2015-11-17T12:57:31Z

Please use rebase --interactive to squash the commits with messages like "" or see last commit.

simonharrer · 2015-11-17T12:57:52Z

src/test/java/net/sf/jabref/importer/fileformat/MedlinePlainImporterTest.java

+
+        //Test with txt File who is in recognized Format
+        Assert.assertTrue(Testimporter
+                .isRecognizedFormat(MedlinePlainImporter.class.getResourceAsStream("MedlinePlainImporterTest.txt")));


Please see #310 for how to handle tests for this part.

koppor · 2015-11-17T13:40:07Z

@boceckts java.lang.StringIndexOutOfBoundsException: String index out of range: -1 during test. Please fix 😇

koppor · 2015-11-21T22:20:49Z

@boceckts Please squash the whole branch history into one commit. The magic command is git rebase master. See #379 (comment) for a longer discussion.

boceckts · 2015-11-22T11:14:03Z

Commits sind nun zu einem Commit zusammengefasst, index out of bounds exception gefixt und die Testmethoden sind nun leicht abgeändert zu AssertEquals.

koppor · 2015-11-22T12:05:45Z

Commit looks good 👍, but the test fail. Could you please investigate?

boceckts · 2015-11-22T12:26:27Z

Welche Tests genau? Wenn ich die Klasse MedlinePlainImporterTest.java als JUnit Test ausführe, laufen alle Test bei mir ohne Fehler..

simonharrer · 2015-11-22T12:55:37Z

src/main/java/net/sf/jabref/importer/fileformat/MedlinePlainImporter.java

@@ -99,7 +99,7 @@ public boolean isRecognizedFormat(InputStream stream) throws IOException {

        for (String entry1 : entries) {

-            if (entry1.trim().isEmpty()) {
+            if (entry1.trim().isEmpty() || (entry1.indexOf('-') < 0)) {


!contains is better readable then indexOf, I think.

koppor · 2015-11-22T14:34:46Z

Siehst du hier beim Pull-Request die Meldung "All checks have failed"? Screenshot:

Du kannst dann auf "Details" bei "ci/circleci" klicken. Dort steht dann "junit failures: testIsRecognizedFormat - in net.sf.jabref.importer.fileformat.MedlinePlainImporterTest". Hier kannst du auf "more info" klicken. Da steht dann

java.lang.NullPointerException
    at java.io.Reader.<init>(Reader.java:78)
    at java.io.InputStreamReader.<init>(InputStreamReader.java:97)
    at net.sf.jabref.importer.ImportFormatReader.getReaderDefaultEncoding(ImportFormatReader.java:352)
    at net.sf.jabref.importer.fileformat.MedlinePlainImporter.isRecognizedFormat(MedlinePlainImporter.java:69)
    at net.sf.jabref.importer.fileformat.MedlinePlainImporterTest.testIsRecognizedFormat(MedlinePlainImporterTest.java:50)

boceckts · 2015-11-22T16:55:05Z

@simonharrer changed it to !contains.
@koppor Seems like one character in the name of the test file was a different case than what I wrote in the java test class.

koppor · 2015-11-22T20:18:06Z

Your test file looks good. Seems to cover seven different entry types with different fields and different settings (doi, multine line titles). However, your test only treats two of them. Why don't you check all test entries?

You could check the result via prepared bibtex files. See https://github.com/JabRef/jabref/blob/6293b4d8ee9409afb25b402643a31904b56e33a0/src/test/java/net/sf/jabref/importer/fetcher/GVKParserTest.java. We are trying to get #378 through so that others can use these test improvements, too.

koppor · 2015-11-26T09:37:20Z

@boceckts We are ready to go from our side. Please have a look at GVKParserTest.java.

boceckts · 2015-12-16T10:35:18Z

The Unit Test failes because multiple comments are being imported with a newline separator. However in the bibtex source the new lines are being ommitted therefore the assertion fails when testing with a import file using multiple comments such as "MedlinePlainImporterTest2.txt vs MedlinePlainImporterTestBib2.bib".

simonharrer · 2015-12-21T13:53:01Z

src/test/java/net/sf/jabref/importer/fileformat/MedlinePlainImporterTest.java

+    public void testEmptyImport() throws Exception {
+        //Test entries with empty txt File
+        List<BibEntry> emptyEntries = importer.importEntries(
+                MedlinePlainImporter.class.getResourceAsStream("MedlinePlainImporterTestEmpty.txt"),


Always use try-with-resources for getResourceAsStream usages.

tobiasdiez · 2015-12-21T16:38:43Z

src/test/java/net/sf/jabref/importer/fileformat/MedlinePlainImporterTest.java

+            }
+        }
+
+        list = Arrays.asList("MedlinePlainImporterTest.txt", "MedlinePlainImporterTest1.txt",


Split tests. Definitely a separate test for recognized and one for not-recognized files. I would even say that there should be a separate test for every file (maybe not for all files, just the ones which actually test a new behavior...say one for txt files and one for isi).

Split tests is a great idea. I think one test method for isRecognized and one for isNotRecognized should be enough since this methods should not test any data but only check if the format is recognized or not.

Yes, you are right, normally one should be enough. But have a look at the isRecognized method and see if you cover all cases. Also it does not harm to check edge cases, like empty files.

tobiasdiez · 2015-12-21T16:58:24Z

Good work 👍 .
Some tests are hard to read since they compare a medline import with a bib import. So it may be hard to see why they fail.

Better test specific features in small test cases (and maybe leave one big "integration" test). For example, (using pseudo-code)

public importParsesDoi() {
  Stream stream = StreamFromString("PMID-22664220" + "\n" + "AID - doi:10.1016/j.cpr.2005.02.002");
  List<Entries> entries = Import(stream);

  BibEntry expected = new BibEntry();
  expected.setField("doi", "10.1016/j.cpr.2005.02.002"); 
  Assert(entries = Collections.singletonList(expected));
}

could replace the test 4. See also https://github.com/JabRef/jabref/wiki/Code-Howtos#test-cases and http://stackoverflow.com/questions/782178/how-do-i-convert-a-string-to-an-inputstream-in-java.

koppor · 2015-12-23T15:57:17Z

Your test fail, because equals is not working on the canonical representation. We are afraid that changing equals (and hashCode) leads to unwanted side effects.

Therefore, please add a method to BibtexEntryAssert for comparing Lists (please use the List interface, not the ArrayList implementation). There, you can use assertEquals(BibEntry shouldBeEntry, BibEntry entry) for comparing the entries themselves.

koppor · 2015-12-23T17:27:20Z

Please also try to get rid of the warnings by eclipse. I think try-with-resources is the solution, isn't it?

boceckts · 2015-12-24T12:08:26Z

#579

boceckts · 2015-12-31T11:20:51Z

Added more test methodes to cover more if conditions and included the suggestions of the comments.

tobiasdiez · 2016-01-02T20:30:33Z

src/test/java/net/sf/jabref/importer/fileformat/MedlinePlainImporterTest.java

+    public void testGetFormatName() {
+        Assert.assertNotEquals("", importer.getFormatName());
+        Assert.assertNotEquals("medlineplain", importer.getFormatName());
+        Assert.assertEquals("MedlinePlain", importer.getFormatName());


Only the last (positive) assert statement is necessary.

tobiasdiez · 2016-01-02T20:33:47Z

Looks very good to me! I just pointed out some smaller things. If they are fixed, this can be merged in (from my point of view).

boceckts · 2016-01-06T20:20:00Z

Thank you for the comments, I removed the unnecessary NotEquals and added tests for the remaining entries in the test file.

- Test import and resulting bibtex files added - Testing imported entries vs bibtex files - Fixed IndexOutOfBoundsExeption - Fixed unreachable Code

koppor · 2016-01-07T07:13:34Z

Coverage 98.65%. I assume that covering line 126 was difficult, because there is no entry where the fourth character of the second line is NOT -. Or similar 😃

Medline plain importer test

simonharrer added stupro labels Nov 17, 2015

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boceckts force-pushed the MedlinePlainImporterTest branch from e373db3 to 92f2318 Compare November 22, 2015 11:00

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boceckts force-pushed the MedlinePlainImporterTest branch 2 times, most recently from 3278d90 to 5b50388 Compare November 22, 2015 16:50

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boceckts force-pushed the MedlinePlainImporterTest branch from 4155d5f to 33382d0 Compare December 16, 2015 10:23

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simonharrer reviewed Dec 21, 2015
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tobiasdiez reviewed Dec 21, 2015
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tobiasdiez mentioned this pull request Dec 21, 2015

Endnote importer test #321

Merged

boceckts force-pushed the MedlinePlainImporterTest branch 2 times, most recently from a9eda92 to 1f08f0c Compare December 22, 2015 12:35

boceckts force-pushed the MedlinePlainImporterTest branch 2 times, most recently from d5b2c18 to 5c7f342 Compare December 24, 2015 12:05

boceckts force-pushed the MedlinePlainImporterTest branch from ea200ff to db9c5b3 Compare December 28, 2015 10:39

koppor added the status: ready-for-review Pull Requests that are ready to be reviewed by the maintainers label Dec 31, 2015

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boceckts force-pushed the MedlinePlainImporterTest branch from db9c5b3 to 4568400 Compare January 6, 2016 20:09

Created MedlinePlainImporter test class

6d09b72

- Test import and resulting bibtex files added - Testing imported entries vs bibtex files - Fixed IndexOutOfBoundsExeption - Fixed unreachable Code

boceckts force-pushed the MedlinePlainImporterTest branch from 4568400 to 6d09b72 Compare January 6, 2016 20:55

koppor added a commit that referenced this pull request Jan 7, 2016

Merge pull request #354 from boceckts/MedlinePlainImporterTest

f1d7c2b

Medline plain importer test

koppor merged commit f1d7c2b into JabRef:master Jan 7, 2016

koppor removed the status: ready-for-review Pull Requests that are ready to be reviewed by the maintainers label Jan 7, 2016

boceckts deleted the MedlinePlainImporterTest branch January 11, 2016 13:38

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Medline plain importer test #354

Medline plain importer test #354

boceckts commented Nov 17, 2015

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Medline plain importer test #354

Medline plain importer test #354

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